Two whistleblowers at a Long Island PETCO store ruffled feathers by alerting an animal-rights group that up to 40 small animals died of heat exposure and trauma when their shop’s air conditioning went on the fritz.

“The stress and heat caused the deaths of many animals,” the workers said in an e-mail to People for the Ethical Treatment of Animals.

PETCO spokesman Dan Cowan acknowledged yesterday that a number of animals died Friday at the chain’s store in Glen Cove.

“We don’t know the exact numbers, but if it’s only one, it’s one too many.”

He said the company has procedures to evacuate animals from its stores in emergencies and was trying to determine if those procedures were followed.

PETA spokeswoman Laura Brown said the death toll included 27 parakeets; three guinea pigs; one hamster and two rats.

The whistleblower had said the casualties were “finches, all of the parakeets, love birds, canaries, cockatiels, guinea pigs . . .”

Cowan said the company had launched an investigation to determine the animals’ exact cause of death.

According to one of the anonymous workers, the animals died after the store’s air-conditioning broke down and a decision was made to transport them to another PETCO location.

The employee claimed that some of the animals, many of whom are sensitive to changes in temperature, were placed in cardboard boxes and transported in employees’ private cars.

The e-mailer said the temperature was 90-plus at the time.

Brown said temperatures inside a parked car – even with the windows open – can quickly exceed 160 degrees.

Cowan said that the only animals still living in the shop are reptiles – cold-blooded creatures who don’t mind the heat. They’re being kept company by fish, whose water temperature is regulated by thermostats.

He said once the air conditioner is fixed, sometime at the end of the week, the store will be restocked.